Dear Sir
I have one query. While we execute MMGBSA/MMPBSA using the following file
Can you tell me how do we make protein-ligand pair for print residue. I am
sending you the minimized file for protein-ligand complex. Kindly guide me
with the residue paring.
Input file for running PB and GB in serial
&general
startframe=1, endframe=5000, interval=50,keep_file=0,
/
&gb
igb=5,saltcon=0.15,
/
&decomp
idecomp=1,
print_res="",
dec_verbose=1,csv_format=0,
Here are few residue list for protein-ligand file........
ATOM 14219 HB3 ALA 902 52.835 -27.895 20.657 1.00 0.00
H
ATOM 14220 C ALA 902 53.875 -26.596 17.594 1.00 0.00
C
ATOM 14221 O ALA 902 54.905 -26.984 17.041 1.00 0.00
O
ATOM 14222 N LYS 903 52.849 -26.019 16.939 1.00 0.00
N
ATOM 14223 H LYS 903 52.069 -25.743 17.524 1.00 0.00
H
ATOM 14224 CA LYS 903 52.710 -25.726 15.490 1.00 0.00
C
ATOM 14225 HA LYS 903 51.689 -25.373 15.336 1.00 0.00
H
ATOM 14226 CB LYS 903 53.641 -24.571 15.071 1.00 0.00
C
ATOM 14227 HB2 LYS 903 54.679 -24.857 15.246 1.00 0.00
H
ATOM 14228 HB3 LYS 903 53.513 -24.399 14.000 1.00 0.00
H
ATOM 14229 CG LYS 903 53.357 -23.254 15.807 1.00 0.00
C
ATOM 14230 HG2 LYS 903 52.322 -22.959 15.629 1.00 0.00
H
ATOM 14231 HG3 LYS 903 53.516 -23.397 16.875 1.00 0.00
H
ATOM 14232 CD LYS 903 54.294 -22.143 15.317 1.00 0.00
C
ATOM 14233 HD2 LYS 903 55.327 -22.436 15.511 1.00 0.00
H
ATOM 14234 HD3 LYS 903 54.158 -22.003 14.243 1.00 0.00
H
ATOM 14235 CE LYS 903 53.990 -20.829 16.045 1.00 0.00
C
ATOM 14236 HE2 LYS 903 52.953 -20.546 15.843 1.00 0.00
H
ATOM 14237 HE3 LYS 903 54.087 -20.991 17.123 1.00 0.00
H
ATOM 14238 NZ LYS 903 54.909 -19.745 15.608 1.00 0.00
N
ATOM 14239 HZ1 LYS 903 54.828 -19.574 14.615 1.00 0.00
H
ATOM 14240 HZ2 LYS 903 54.704 -18.876 16.084 1.00 0.00
H
ATOM 14241 HZ3 LYS 903 55.873 -19.980 15.802 1.00 0.00
H
ATOM 14242 C LYS 903 52.857 -26.923 14.531 1.00 0.00
C
ATOM 14243 O LYS 903 51.893 -27.266 13.840 1.00 0.00
O
ATOM 14244 N ALA 904 54.043 -27.539 14.506 1.00 0.00
N
ATOM 14245 H ALA 904 54.707 -27.200 15.190 1.00 0.00
H
ATOM 14246 CA ALA 904 54.531 -28.559 13.565 1.00 0.00
C
ATOM 14247 HA ALA 904 55.586 -28.704 13.800 1.00 0.00
H
ATOM 14248 CB ALA 904 53.832 -29.896 13.865 1.00 0.00
C
ATOM 14249 HB1 ALA 904 52.791 -29.856 13.543 1.00 0.00
H
ATOM 14250 HB2 ALA 904 54.336 -30.702 13.331 1.00 0.00
H
ATOM 14251 HB3 ALA 904 53.870 -30.109 14.935 1.00 0.00
H
ATOM 14252 C ALA 904 54.515 -28.141 12.069 1.00 0.00
C
ATOM 14253 O ALA 904 54.218 -26.966 11.750 1.00 0.00
O
ATOM 14254 OXT ALA 904 54.872 -28.985 11.215 1.00 0.00
O
TER
ATOM 14255 C1 DRG 905 27.937 -18.959 31.838 1.00 0.00
C
ATOM 14256 C2 DRG 905 29.114 -18.282 31.537 1.00 0.00
C
ATOM 14257 C3 DRG 905 30.190 -18.966 30.984 1.00 0.00
C
ATOM 14258 C4 DRG 905 30.116 -20.352 30.814 1.00 0.00
C
ATOM 14259 C5 DRG 905 28.966 -21.040 31.192 1.00 0.00
C
ATOM 14260 C6 DRG 905 27.849 -20.339 31.652 1.00 0.00
C
ATOM 14261 C7 DRG 905 26.554 -21.000 31.913 1.00 0.00
C
ATOM 14262 C8 DRG 905 26.209 -22.297 31.850 1.00 0.00
C
ATOM 14263 C9 DRG 905 24.871 -22.885 32.088 1.00 0.00
C
ATOM 14264 O1 DRG 905 24.717 -24.093 32.045 1.00 0.00
O
ATOM 14265 C10 DRG 905 23.719 -21.946 32.424 1.00 0.00
C
ATOM 14266 O2 DRG 905 23.171 -21.264 31.255 1.00 0.00
O
ATOM 14267 C11 DRG 905 22.243 -20.145 31.445 1.00 0.00
C
ATOM 14268 C12 DRG 905 21.355 -20.266 32.711 1.00 0.00
C
ATOM 14269 C13 DRG 905 20.290 -19.130 32.811 1.00 0.00
C
ATOM 14270 C14 DRG 905 21.009 -17.751 32.704 1.00 0.00
C
ATOM 14271 C15 DRG 905 21.929 -17.613 31.465 1.00 0.00
C
ATOM 14272 C16 DRG 905 22.963 -18.770 31.364 1.00 0.00
C
ATOM 14273 O3 DRG 905 23.945 -18.606 32.408 1.00 0.00
O
ATOM 14274 O4 DRG 905 21.078 -17.589 30.319 1.00 0.00
O
ATOM 14275 C17 DRG 905 19.500 -19.163 34.155 1.00 0.00
C
ATOM 14276 O5 DRG 905 20.037 -19.600 35.173 1.00 0.00
O
ATOM 14277 O6 DRG 905 18.417 -18.618 34.223 1.00 0.00
O
ATOM 14278 O7 DRG 905 19.415 -19.228 31.626 1.00 0.00
O
ATOM 14279 C18 DRG 905 18.457 -20.333 31.538 1.00 0.00
C
ATOM 14280 C19 DRG 905 18.367 -20.983 30.159 1.00 0.00
C
ATOM 14281 O8 DRG 905 17.606 -21.907 29.934 1.00 0.00
O
ATOM 14282 C20 DRG 905 19.252 -20.458 29.095 1.00 0.00
C
ATOM 14283 C21 DRG 905 19.352 -20.825 27.808 1.00 0.00
C
ATOM 14284 C22 DRG 905 20.216 -20.204 26.776 1.00 0.00
C
ATOM 14285 C23 DRG 905 21.232 -19.302 27.125 1.00 0.00
C
ATOM 14286 C24 DRG 905 22.006 -18.677 26.151 1.00 0.00
C
ATOM 14287 C25 DRG 905 21.770 -18.952 24.811 1.00 0.00
C
ATOM 14288 C26 DRG 905 20.776 -19.864 24.458 1.00 0.00
C
ATOM 14289 C27 DRG 905 20.007 -20.499 25.427 1.00 0.00
C
ATOM 14290 O9 DRG 905 20.595 -20.112 23.141 1.00 0.00
O
ATOM 14291 O10 DRG 905 22.510 -18.342 23.836 1.00 0.00
O
ATOM 14292 O11 DRG 905 31.142 -21.024 30.221 1.00 0.00
O
ATOM 14293 O12 DRG 905 31.283 -18.254 30.573 1.00 0.00
O
ATOM 14294 H1 DRG 905 27.079 -18.402 32.212 1.00 0.00
H
ATOM 14295 H2 DRG 905 29.175 -17.211 31.699 1.00 0.00
H
ATOM 14296 H3 DRG 905 28.931 -22.114 31.064 1.00 0.00
H
ATOM 14297 H4 DRG 905 25.775 -20.290 32.176 1.00 0.00
H
ATOM 14298 H5 DRG 905 26.981 -23.016 31.593 1.00 0.00
H
ATOM 14299 H6 DRG 905 22.936 -22.547 32.894 1.00 0.00
H
ATOM 14300 H7 DRG 905 24.091 -21.213 33.138 1.00 0.00
H
ATOM 14301 H8 DRG 905 21.584 -20.194 30.578 1.00 0.00
H
ATOM 14302 H9 DRG 905 20.873 -21.237 32.721 1.00 0.00
H
ATOM 14303 H10 DRG 905 21.987 -20.220 33.594 1.00 0.00
H
ATOM 14304 H11 DRG 905 20.262 -16.954 32.688 1.00 0.00
H
ATOM 14305 H12 DRG 905 21.601 -17.588 33.604 1.00 0.00
H
ATOM 14306 H13 DRG 905 22.473 -16.665 31.515 1.00 0.00
H
ATOM 14307 H14 DRG 905 23.469 -18.703 30.395 1.00 0.00
H
ATOM 14308 H15 DRG 905 23.468 -18.457 33.265 1.00 0.00
H
ATOM 14309 H16 DRG 905 20.279 -18.105 30.615 1.00 0.00
H
ATOM 14310 H17 DRG 905 18.721 -21.123 32.238 1.00 0.00
H
ATOM 14311 H18 DRG 905 17.460 -19.958 31.784 1.00 0.00
H
ATOM 14312 H19 DRG 905 19.883 -19.639 29.393 1.00 0.00
H
ATOM 14313 H20 DRG 905 18.658 -21.588 27.448 1.00 0.00
H
ATOM 14314 H21 DRG 905 21.454 -19.078 28.163 1.00 0.00
H
ATOM 14315 H22 DRG 905 22.791 -17.987 26.449 1.00 0.00
H
ATOM 14316 H23 DRG 905 19.232 -21.198 25.123 1.00 0.00
H
ATOM 14317 H24 DRG 905 21.309 -19.559 22.740 1.00 0.00
H
ATOM 14318 H25 DRG 905 23.296 -17.874 24.215 1.00 0.00
H
ATOM 14319 H26 DRG 905 31.772 -20.337 29.892 1.00 0.00
H
ATOM 14320 H27 DRG 905 30.967 -17.378 30.223 1.00 0.00
H
TER
END
I request you to kindly guide me in making protein-ligand pair.
Thanks
Arunima
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Received on Mon May 26 2014 - 21:00:03 PDT
